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protocols::simple_moves::SimpleThreadingMover Class Reference

This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling. More...

#include <SimpleThreadingMover.hh>

Inheritance diagram for protocols::simple_moves::SimpleThreadingMover:
Inheritance graph
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Public Member Functions

 SimpleThreadingMover ()
 
 SimpleThreadingMover (std::string thread_sequence, core::Size start_position)
 
 SimpleThreadingMover (SimpleThreadingMover const &src)
 
 ~SimpleThreadingMover () override
 
void set_sequence (std::string thread_sequence, core::Size start_position)
 Set the sequence to thread onto the structure used in apply and where to start. More...
 
void set_pack_neighbors (bool pack_neighbors)
 Pack the neighbor residues? More...
 
void set_neighbor_distance (core::Real neighbor_dis)
 Set the packing distance for neighbor pack. More...
 
bool get_pack_neighbors () const
 
core::Real get_neighbor_distance () const
 
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
 Set the scorefunction used for packing. More...
 
void set_pack_rounds (core::Size pack_rounds)
 Set the number of pack rounds. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide a list of authors and their e-mail addresses, as strings. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Member Functions

void set_defaults ()
 

Private Attributes

core::Size start_position_
 
std::string thread_sequence_
 
bool pack_neighbors_
 
core::Real neighbor_dis_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
std::string parsed_position_
 
bool skip_unknown_mutant_
 
core::Size pack_rounds_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Detailed Description

This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling.

It does the threading by allowing the task to only enable these residues and then does a repacking. Optionally repack neighbors so we save one more step. A sequence is just a string, additional '-' charactors denote to skip this position in the thread. Default is 5 rounds of packing.

Constructor & Destructor Documentation

protocols::simple_moves::SimpleThreadingMover::SimpleThreadingMover ( )

References set_defaults().

protocols::simple_moves::SimpleThreadingMover::SimpleThreadingMover ( std::string  thread_sequence,
core::Size  start_position 
)

References set_defaults(), and thread_sequence_.

protocols::simple_moves::SimpleThreadingMover::SimpleThreadingMover ( SimpleThreadingMover const &  src)
default
protocols::simple_moves::SimpleThreadingMover::~SimpleThreadingMover ( )
overridedefault

Member Function Documentation

void protocols::simple_moves::SimpleThreadingMover::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::simple_moves::SimpleThreadingMover::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

moves::MoverOP protocols::simple_moves::SimpleThreadingMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::simple_moves::SimpleThreadingMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

core::Real protocols::simple_moves::SimpleThreadingMover::get_neighbor_distance ( ) const

References neighbor_dis_.

bool protocols::simple_moves::SimpleThreadingMover::get_pack_neighbors ( ) const

References pack_neighbors_.

std::string protocols::simple_moves::SimpleThreadingMover::mover_name ( )
static
bool protocols::simple_moves::SimpleThreadingMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Reimplemented from protocols::moves::Mover.

void protocols::simple_moves::SimpleThreadingMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References neighbor_dis_, pack_neighbors_, pack_rounds_, core::scoring::parse_score_function(), parsed_position_, scorefxn_, skip_unknown_mutant_, and thread_sequence_.

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::simple_moves::SimpleThreadingMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Reimplemented from protocols::moves::Mover.

References mover_name().

void protocols::simple_moves::SimpleThreadingMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_moves::SimpleThreadingMover::set_defaults ( )
private
void protocols::simple_moves::SimpleThreadingMover::set_neighbor_distance ( core::Real  neighbor_dis)

Set the packing distance for neighbor pack.

References neighbor_dis_.

void protocols::simple_moves::SimpleThreadingMover::set_pack_neighbors ( bool  pack_neighbors)

Pack the neighbor residues?

References pack_neighbors_.

void protocols::simple_moves::SimpleThreadingMover::set_pack_rounds ( core::Size  pack_rounds)

Set the number of pack rounds.

References pack_rounds_.

void protocols::simple_moves::SimpleThreadingMover::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)

Set the scorefunction used for packing.

References scorefxn_.

void protocols::simple_moves::SimpleThreadingMover::set_sequence ( std::string  thread_sequence,
core::Size  start_position 
)

Set the sequence to thread onto the structure used in apply and where to start.

Can have '-' charactors in sequence to denote a gap in the threaded sequence.

References start_position_, and thread_sequence_.

Member Data Documentation

core::Real protocols::simple_moves::SimpleThreadingMover::neighbor_dis_
private
bool protocols::simple_moves::SimpleThreadingMover::pack_neighbors_
private
core::Size protocols::simple_moves::SimpleThreadingMover::pack_rounds_
private
std::string protocols::simple_moves::SimpleThreadingMover::parsed_position_
private

Referenced by apply(), parse_my_tag(), and set_defaults().

core::scoring::ScoreFunctionCOP protocols::simple_moves::SimpleThreadingMover::scorefxn_
private
bool protocols::simple_moves::SimpleThreadingMover::skip_unknown_mutant_
private

Referenced by apply(), parse_my_tag(), and set_defaults().

core::Size protocols::simple_moves::SimpleThreadingMover::start_position_
private

Referenced by apply(), and set_sequence().

std::string protocols::simple_moves::SimpleThreadingMover::thread_sequence_
private

The documentation for this class was generated from the following files: